DNA Confined in a Nanodroplet: A Molecular Dynamics Study

Abstract

As a major genetic material, the configuration and the mechanical properties of a double-stranded DNA (dsDNA) molecule in confinement are crucial for the application of nanotechnology and biological engineering. In the present paper, molecular dynamics simulation is utilized to study the configuration of dsDNA in a nanodroplet on a graphene substrate. The results show that the semiflexible dsDNA molecule changes its configuration with radius of gyration ( R) of a few nanometers because of the confined space, that is, the R of the dsDNA molecule decreases with the reduction of the nanodroplet size. In comparison, the dsDNA in the bulk usually has a persistent length of tens of nanometers. Especially, if the nanodroplet is small enough, the dsDNA molecule might form a loop structure inside. The dsDNA molecule affects the wetting properties of the graphene substrate. It is found that the graphene becomes more hydrophilic in smaller systems containing the dsDNA molecule, whereas for larger droplets, the changes of the contact angles are not significant with the presence of dsDNA. Moreover, the results indicate that for larger droplets, the line tension of the droplet containing DNA is positive and greater than that without DNA; for smaller droplets, the line tension becomes negative because the dsDNA is compressed and bent in the confinement, and has the potential to expand outwards. The worm-like chain model is used to study the bending energy of a dsDNA molecule in a droplet. The results address that the bending energy of the non-loop-structured dsDNA decreases as the droplet becomes larger, and it is larger than that of loop-structured dsDNA, as the loop structure efficiently prevents the DNA from bending in the vertical direction.

Modulation of DNA conformation in electrolytic nanodroplets

“…3(b), the radius of gyration R g always increases as the nanodroplets become larger, which is consistent with our previous investigation. 60 It should be noted that when the radius of the smallest nanodroplet r d is about 4.5 nm, R g can be as small as about 3 nm. Meanwhile, for the largest nanodroplet we simulated with r d = 11.4 nm, R g is approximately 6 nm.…”

“…The external load or the compression on DNA can be regulated by the nanodroplet size. In our recent investigation, 60 we explored the effects of the nanodroplet size on the conformation of dsDNA confined in pure water nanodroplets and found that the dsDNA in nanodroplets of different volumes exhibits different conformations. The theoretical prediction of the polymer stiffness in an ionic solution is still a challenging issue although extensive research has been performed in previous studies.…”

Pressure of Linear and Ring Polymers Confined in a Cavity

“…However, moderately confined polymers in our snapshots feature the toroids in various degrees of development, involving the less organized segments. Interestingly, the simulation of short DNA confined in nanodroplets with different volumes on a graphene substrate 5 nanodroplets of size only a few nanometers, finally resulting in a loop structure inside a nanodroplet. At strong confinement of long semiflexible chains, concentrations much above φ ∼ 0.1 are encountered.…”

“…Interaction with the confining boundaries greatly affects the properties and spatial organization of polymers. , The confinement effects are eminent at the entrapment of a single polymer inside a closed cavity, denoted as volume confinement. The examples of volume confinement in the biological and nanotechnology milieu include biopolymers in subcellular structures such as the double-stranded (ds)­DNA in viral capsids, the double-nanopore architecture used for DNA sensing, polymers confined in (nano)­droplets or encapsulated into artificial lipid vesicles such as liposomes, and nanoparticles with unique microphase-separated structures . In contrast to the slits and cylinders, the confinement of a polymer in cavities of the spherical or comparable native shapes drastically restricts the conformational space available to a polymer.…”